Could definitely be a ground issue. You could check all of your grounds and make sure they're proper grounds and that they're very clean. If the system has been installed for a long time, there could be some corrosion on the amp ground or even the head unit ground.
Sometimes, if the head unit isn't grounded properly, it will get its ground through the antenna wire but since that's not a good ground either, it can cause some damage that doesn't materialize immediately.
I'd go through all of my grounds and power connections meticulously, even if I had just installed the system. I've been pulling wire and hooking things up for over 25 years and I make mistakes or overlook something on occasion... maybe a ground isn't tight, maybe the ground on the head unit has some current floating on it, the maybes are a plenty.